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1. ⭐ GSE298839 组蛋白甲基转移酶 Ezh2 的缺失加剧了肝细胞癌中巨噬细胞向 M2 样表型的极化 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、ATAC-seq、histone
• 📝 描述：Contributors : Kittin Weerasopon ; Atsadang Boonmee ; Patipark Kueanjinda ; Benjawan Wongprom ; Thitiporn Pattarakankul ; Tanapat PalagaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe roles of epigenetic regulator Ezh2 in TAMs of liver cancer still unclear. In this study, our results demonstrated that the absence of Ezh2 in bone marrow-derived macrophages (BMDMs) exacerbated M2-like phenotypic changes upon incubation with conditioned media (CM) from hepatocellular carcinoma (HCC) cell line Hepa1-6. The ATAC-seq revealed that the promoter regions of pyruvate metabolic process-related genes were more accessible in treated BMDMs Ezh2 KO.
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2. ⭐ GSE298836 组蛋白甲基转移酶 Ezh2 的缺失加剧了肝细胞癌中巨噬细胞向 M2 样表型的极化 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、RNA-seq、histone
• 📝 描述：Contributors : Kittin Weerasopon ; Atsadang Boonmee ; Patipark Kueanjinda ; Benjawan Wongprom ; Thitiporn Pattarakankul ; Tanapat PalagaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe roles of histone methytransferase Ezh2 in TAMs of liver cancer still unclear. In this study, an RNA sequencing was performed for samples from bone marrow-derived macrophages (BMDMs) of WT and Ezh2 KO mice upon exposure to conditioned media (CM) from hepatocellular carcinoma (HCC) cell line Hepa1-6. The results demonstrated that the absence of Ezh2 in BMDMs exacerbated M2-like phenotypic changes upon incubation with CM from hepatocellular carcinoma (HCC) cell line. The RNA-sequencing revealed that the M2 gene set was further upregulated in treated BMDMs Ezh2 KO compared to treated BMDMs WT WT and the hallmark of Glycolysis as enriched pathway was identified in BMDMs Ezh2 KO. Additionally, the hallmark of IL-6/JAK/STAT pathway was enriched in CM-treated BMDMs. Collectively, these findings provide evidence that JAK/STAT3 axis is critical for M2-like phenotypic changes and Ezh2 suppresses the shifts of macrophage metabolism toward glycolysis that promotes M2 polarization.
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3. GSE306716 单细胞 RNA 测序揭示了 MMTV-R26Met 同源 TNBC 模型中的细胞和分子异质性以及不同的免疫抑制特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Olivier Castellanet ; Jean Monatte ; Paula Michea ; Julien Vernerey ; Flavio Maina ; Fabienne LamballeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTriple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer with limited targeted therapies. To model TNBC heterogeneity in an immunocompetent setting, we established syngeneic grafts derived from the TNBC MMTV-R26Met genetically engineered mouse model, which preserve both the molecular identity and immune landscape of primary tumors. These grafts recapitulate features of distinct TNBC subtypes, providing a physiologically relevant preclinical platform to investigate tumor–immune interactions and therapy response. Here, we performed single-cell RNA sequencing (scRNA-seq) on four syngeneic tumors (S34, S35, S37, and S39), generating transcriptomic profiles from 22,046 cells. Clustering identified cell populations spanning malignant epithelial, stromal, endothelial, and diverse immune subsets. Tumors displayed subtype-specific traits, including oxidative phosphorylation programs with N2-like neutrophils and epithelial–mesenchymal transition with M2-like macrophages. Despite overall low T cell infiltration, inhibitory receptors and myeloid checkpoint ligands were broadly expressed, highlighting strongly immunosuppressive microenvironments. These datasets provide a resource for dissecting TNBC subtype heterogeneity in an immunocompetent context and offer a preclinical framework to explore mechanisms of immune evasion and therapeutic response.
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4. GSE298709 BAFF-R 表达作为抗体缺乏患者 COVID-19 疫苗无应答的预测生物标志物

• ✍️ 作者：未知作者
• 🏷️ 关键词：vaccine、antibody
• 📝 描述：Contributors : Eleanor O’Callaghan ; Adrian Shields ; Leon Chang ; Michelle Umpierrez ; Siobhan O Burns ; Alex G Richter ; Gina Doody ; Sinisa SavicSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPatients with primary and secondary antibody deficiencies exhibit variable responses to vaccination, with a substantial proportion failing to mount protective immunity to SARS-CoV-2. Mechanisms underpinning vaccine non-responsiveness in this population remain poorly defined. Our objective was to investigate B-cell-intrinsic defects underlying SARS-CoV-2 vaccine failure by assessing the capacity for plasma cell differentiation in a heterogeneous cohort of antibody-deficient patients using an in vitro model.
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5. GSE319900 李施德林® 可减轻细胞因子诱导的炎症并激活牙龈成纤维细胞中的锌-金属硫蛋白反应

• ✍️ 作者：未知作者
• 🏷️ 关键词：cytokine、inflammation
• 📝 描述：Contributors : Anna Podesser ; Xiaoyu Huang ; Panahipour Layla ; Reinhard GruberSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGingival fibroblasts amplify periodontal inflammation by producing chemokines in response to pro-inflammatory cytokines. Mouth rinses directly contact the gingival tissues, yet their effects on host inflammatory signaling remain incompletely defined. This study investigated how a zinc-containing Listerine® formulation modulates IL-1β/TNF-α–induced responses in human gingival fibroblasts and compared these effects with zinc alone. Primary human gingival fibroblasts were stimulated with IL-1β and TNF-α in the presence or absence of Listerine®. Global transcriptional changes were analyzed by RNA sequencing and validated by quantitative PCR. CXCL8 secretion was quantified by immunoassay. Zinc ions and individual essential oil components were tested separately. Metal content was determined by inductively coupled plasma–mass spectrometry. IL-1β/TNF-α induced a broad inflammatory transcriptional program, including chemokines and innate immune–associated genes. Co-treatment with Listerine® consistently reduced the magnitude of cytokine-induced gene expression while preserving inducibility, indicating quantitative attenuation rather than suppression. Listerine® significantly decreased cytokine-induced CXCL1, CXCL2, and CXCL8 mRNA levels and reduced CXCL8 protein release. Transcriptomic profiling revealed strong induction of metallothionein family members. Zinc was identified as the predominant metal at biologically relevant concentrations. Zinc alone robustly induced metallothioneins but did not significantly reduce cytokine-induced chemokine expression. Individual essential oil components did not reproduce the inhibitory effect. Taken together, Listerine® constrains cytokine-driven inflammatory output in gingival fibroblasts while activating a zinc-associated metallothionein stress response. Zinc alone is insufficient to explain the anti-inflammatory phenotype, supporting a formulation-dependent host-modulating effect.
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6. GSE289928 将靶向 CD33 的嵌合抗原受体 T 细胞与地西他滨联合用于治疗急性髓系白血病

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、antigen
• 📝 描述：Contributors : Tongyuan Xue ; Marissa Del Real ; Jonas J Wu ; Elizabeth L BuddeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground: Relapsed and/or refractory (r/r) acute myeloid leukemia (AML) is a challenging disease with poor prognosis and limited treatment options. CD33, a cell surface antigen expressed on over 85% of AML blasts, is a promising target for chimeric antigen receptor (CAR) T-cell therapy. Decitabine (DAC), a hypomethylating agent (HMA), is a well-tolerated treatment for AML patients. Combining anti-CD33 immunotherapy with HMAs has shown benefits in AML patients unfit for intensive chemotherapy. Our goal is to develop optimal CD33-CAR T cells and combine them with DAC to provide an effective treatment for AML. Methods: Flow cytometry and antibody-binding capacity analysis were used to measure cell surface marker expression. Degranulation, intracellular cytokine expression, and tumor cell killing assays were used to assess CAR-T cell function in vitro. In vivo antileukemic activity was examined in AML xenografted NSG mice, with leukemic burden monitored via bioluminescence imaging. colony-forming-unit assay assessed the impact of CD33-CAR T cells on normal hematopoiesis. Public dataset analysis assessed correlation between two variables, such as CD33 mRNA expression and DNA methylation. Pairwise Controlled Manifold Approximation (PaCMAP) was used to visualized T cell-patient AML blast microenvironment after killing assay. Bulk RNA-seq analyzed mRNA and signaling pathways changes in AML cells after exposure to DAC. Results: We generated CD33-CAR T cells using a humanized anti-CD33 scFv and found that the CD8H version was more potent than the IgG4(EQ) variant against CD33⁺ AML cell lines. The CH8H CAR T cells exhibited strong effector functions and significantly reduced AML tumor burden in NSG mice, without impairing HSPC colony formation. In silico analysis revealed an inverse correlation between CD33 methylation and gene expression. DAC pretreatment upregulated CD33 expression, enhancing AML cell elimination by CD33-CAR T cells in vitro and in vivo, especially under conditions with limited CAR T-cells. DAC upregulated the proteasome inhibition-induced apoptosis pathway and downregulated DNA repair and MYC oncogenic pathways, which, together with enhanced CD33 expression, primed AML cells for more effective CAR T-cell targeting. Conclusions: This study demonstrates the preclinical efficacy and sa…
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7. GSE312416 生酮饮食通过β-羟基丁酸-螺旋丝菌-γδ17 T细胞轴加剧小鼠DSS诱导的结肠炎

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell
• 📝 描述：Contributors : Yameng Liu ; Xuan Wu ; Li Chen ; Shan Wang ; Cen Xie ; Lei Chen ; Weiwei LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusKetogenic diets (KD) benefit metabolic and neurological health by modulating gut microbiota, but their impact on inflammatory bowel disease, particularly ulcerative colitis (UC), remains controversial. Here, we show that KD aggravated colitis by triggering a ketogenesis-microbe-immune cascade. KD elevated luminal β-hydroxybutyrate (β-HB), which fueled the expansion of Thomasclavelia spiroformis (T. spiroformis), a pathobiont that activated mucosal γδ17 T cells potentially via peptidoglycans. These cells drived IL-17A production and inflammation; reconstitution of γδ17 T cells in Tcrd-/- mice confirmed their pathogenic role. Blocking ketogenesis or neutralizing IL-17A abolished KD-exacerbated colitis, whereas β-HB supplementation and ketogenesis activation phenocopied disease worsening. In UC patients, T. spiroformis abundance correlated with fecal β-HB and serum IL-17A levels, but not in Crohn’s disease, supporting a UC-specific β-HB-T. spiroformis-γδ17 T cell axis. These findings uncover a metabolic-microbial-immune loop linking dietary ketosis to UC, and suggest that targeting ketone metabolism or IL-17A signaling may offer new therapeutic opportunities.
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8. GSE305105 丙酮酸脱氢酶激酶4敲除对血管平滑肌细胞功能的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：kinase
• 📝 描述：Contributors : Li Zhao ; Xiu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis study investigated the impact of pyruvate dehydrogenase kinase 4 knockout on the function of vascular smooth muscle cells.
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9. GSE288178 福尔马林固定石蜡包埋组织中染色质景观的空间分辨

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatially
• 📝 描述：Contributors : Haikuo Li ; Rong FanSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusFormalin-fixed paraffin-embedded (FFPE) samples represent an invaluable resource for histopathology research, but chromatin crosslinking in these fixed tissues precludes epigenomic analyses. Here, we present methods for reversing crosslinking in FFPE tissues followed by spatially resolved assay for transposase-accessible chromatin using sequencing (spatial-FFPE-ATAC) or cleavage under targets and tagmentation (spatial-FFPE-CUT&Tag). We applied spatial-FFPE-ATAC on adult mouse brain and revealed region-specific chromatin accessibility profiles with data quality comparable to standard ATAC-seq performed on fresh-frozen samples. Spatial-FFPE-ATAC delineated the epigenetic heterogeneity of clinical archival lymphoma of mucosa-associated lymphoid tissue and follicular lymphoma samples and uncovered tumor-specific karyotypes. Spatial-FFPE-ATAC traced cell proliferation by mitotic age inference and identified cholesterol-mediated cell proliferation in tumor cells. Spatial-FFPE-CUT&Tag in a transformed diffuse large B-cell lymphoma tissue revealed increased H3K27me3 occupancy at a chromosome 2 locus associated with tumor-specific copy number amplification. Therefore, spatial-FFPE-ATAC and spatial-FFPE-CUT&Tag enable genome-wide epigenomic profiling and epigenetic regulation investigations in archival FFPE samples.
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10. GSE269546 丙酮酸脱氢酶激酶4过表达对血管平滑肌细胞功能的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：kinase
• 📝 描述：Contributors : Li Zhao ; Xiu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis study investigated the impact of pyruvate dehydrogenase kinase 4 overexpression on the function of vascular smooth muscle cells.
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1. 这种冰洞细菌在冰封了5000年后，仍然能够抵抗现代抗生素。

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:bacter(ia|ial|ium)
• 📝 描述：Deep inside a Romanian ice cave, locked away in a 5,000-year-old layer of ice, scientists have uncovered a bacterium with a startling secret: it’s resistant to many modern antibiotics. Despite predating the antibiotic era, this cold-loving microbe carries more than 100 resistance-related genes and can survive drugs used today to treat serious infections like tuberculosis and UTIs.
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• GSE298909 Tim-3激动剂通过NLK通路抑制ILC2功能并减弱气道高反应性
• GSE319955 静止的神经干细胞短暂地转变为神经元样细胞，以协调长程重新激活
• GSE319888 TES 和 TEAD1 在 SNB19 胶质母细胞瘤细胞中的转录调控：RNA-seq
• GSE319685 10x 16plex flex scRNAseq，使用来自野生型 (WT) 或 Ccr2-/- 小鼠的未感染或 SARS-CoV-2 感染的小鼠肺组织。
• GSE319684 SARS-CoV-2 (maVie16) 与 IAV (PR8) 感染小鼠肺中 FACS 分选的 Ly6C+ 单核细胞、组织驻留肺泡巨噬细胞 (trAMs)、单核细胞衍生肺泡巨噬细胞 (bmAMs) 和上皮细胞的时间进程
• GSE309776 降解子模型：用于快速体内耗竭调控 mRNA 代谢的必需蛋白的工具箱